City level estimates of the time-varying reproduction number of Covid-19 produced using EpiNow2 based on data from brazil.io. Regional estimates for Brazil (along with a national estimate) are available here. Detail of the method used is given here, though the estimates shown here were derived using an approximate approach (variational inference) rather than the exact method used on epiforecasts.io and therefore should only be considered indicative. The code and data supporting these estimates is available here.
Case data from the last 10 weeks is extracted from: brazil.io
Estimates were only produced for cities with at least 200 cases, and 30 days of data, in the last 10 weeks. All time series were truncated by 3 days to account for delayed reporting (the delay from original report to reporting in this dataset not the adjusted for delay from onset to original report). Estimates are only shown for the last 8 weeks of data combined with a 2 week indicative forecast.
Data on the delay from onset to report were extracted for Brazil from here: github.com/beoutbreakprepared/nCoV2019
Estimates for the incubation period and the generation time were based on those used here: epiforecasts.io